Experiment Detail
| Title | Bacteria in soiled sands experiment (OS-243b) |
| Design Description | These are amplicon sequence libraries of sequences from 250-500 bases, single direction read. Pyrotag sequencing of bacterial small subunit ribosomal RNAs (SSU rRNAs) and SSU rRNA genes was performed using multiplexed, bar-coded primers targeting the V1-V3 region of the bacterial SSU rRNA. |
| Organism | beach sand metagenome |
Library Description
| Name | OS-243b |
| Strategy | AMPLICON |
| Source | METAGENOMIC |
| Selection | PCR |
| Layout | SINGLE |
| Construction Protocol | Genomic DNA was extracted from Pensacola sands using the MoBio Powersoil DNA extraction kit (Mo Bio Laboratories, Carlsbad, CA). RNA was extracted from sand samples according to the method described by Chin et al. 2008 (Microbial Ecology 55:489-499), and reverse transcribed using a general bacterial primer targeting the SSU rRNA. gDNA and cDNA were amplified with primers 28F (GAG TTT GAT CNT GGC TCA G) and 519R (GTN TTA CNG CGG CKG CTG) by the Research and Testing Laboratory (Lubbock, TX, USA). Amplicons were then pooled for Roche 454 pyrotag sequencing using Titanium technology, resulting in single-direction reads on the order of 250-500 bases. |
Platform
| Platform | LS454 |
| Instrument Model | 454 GS FLX Titanium |
Processing
| Base Calls | |
|---|---|
| Sequence Space | |
| Base Caller | |
Spot Information
| Number of Reads per Spots | 0 |
| Spot Length | 0 |
Read Spec
| Read Index 0 | |
|---|---|
| Read Label | |
| Read Class | Application Read |
| Read Type | Forward |
| Base Coord | 1 |
